Hidden Shadow
by Shadow38383
Summary: Red arrives to Orre in search of Leaf. Sorry for short summery.


**This just came to me while playing Pokemon XD. - not a face lol. If its...off or not really...just...if something is nnot clicking then blame my volunteer beta readers! I have not revived a response so I am in search of a new one who cares about fan fiction! Anyways, let me know if its going alright or if I should change things to make it a one shot, enjoy!**

Red stared out at the port he was arriving to on the S.S. Libra, holding a white hat, with a red stripe that out lined the shape of a poke ball, close to his chest.

"Gateon Port is what they called it I think." Red said to himself, "Maybe I'll find her here, in Orre. Two years without her is two years too much." The ship docked at the port and Red got off along with the other passengers. "Maybe I'll find her at Mt. Battle, I heard some trainers talking about it. He was about to start asking for directions to Mt. Battle when a little girl slammed into him and both of them hit the floor.

"Ow ow ow, Jovi fell down." the girl commented.

"I'm...guessing your name is Jovi?" Red asked as he got up and helped her stand.

"That's right! Do you mind if Jovi asks your name?" she asked.

"Uhh...Red." he replied.

"Jovi!" a voice called out. Red turned to the source of the voice to see a boy, possibly about a year or two younger than himself, running up to them, "Jovi, mom told you to stick with me. You remember what happened last time with that Zook guy."

"But that's why you're here big brother, to defend Jovi!" Jovi replied. The boy face palmed.

"Thanks for catching her." the boy commented to Red, "Name's Michael."

"Red." Red replied, "Umm, by the way, do you know how to get to Mt. Battle?"

"Yeah, I go there a lot." Michael replied, "You going to try for a straight through run?"

"Maybe." Red replied as he looked to the ocean's horizon.

"What's this?" Jovi asked as she grabbed the hat from inside Red's backpack.

"No wait!" Red shouted as Jovi ran away with the hat on her head, "Please be careful with it!"

"Can I have it?" Jovi asked, "Jovi likes this ha-" Jovi was cut off as a gust of wind blew the hat off her head and straight into the ocean. Red didn't hesitated and quickly jumped into the water. Fighting against the waves, he swam towards the hat and managed to grab it. Red quickly put away the hat and swam back to shore.

"Red, you ok?" Michael asked. Red quickly pulled out the hat to check for damage.

"Yeah, I'm fine." Red replied with relief as he put the hat away, "Do you visit this port a lot?"

"I run errands here a lot, so yes." Michael replied.

"Have you seen a girl about my age arrive at the port?" Red asked, "Brown hair, blue eyes, really cute?"

"Sorry, but a lot of girls fit that description." Michael replied. Red nodded sadly and prepared to leave, but a scream caused him to stop and turn his attention to the light house. At the top of the light house stood a girl with brown hair, wearing a blue sleeveless shirt, a red skirt, and holding, what appeared to be a Pichu, closely and backing up into the edge like if she was cornered.

"Is that?" Red thought out loud. Michael was about to ask when the girl jumped off the lighthouse. Red didn't hesitate, or even wait for her to come close to the water, before he jumped in. The girl made contact with the water, but she didn't sink far before red pulled her up by the waist and brought her with him to shore.

Michael looked back up at the light house and saw two people wearing a familiar armor-like uniform.

"Leaf!" Red shouted as he lifted the girl up by the shoulders with one arm, "Leaf, are you ok!? Come on, please answer me!" Leaf emitted a moan of dizziness then slowly opened her eyes and looked at Red.

"Who are you?" she asked. Red was shocked, he couldn't tell if she was serious or just confused from the impact with the water.

"Leaf, it's me, Red." Red replied, "Don't you remember? We grew up in Pallet town and traveled the Kanto region together!"

"I...I'm sorry...I don't know who you are." Leaf replied.

'Th-this has to be a dream!' Red thought, 'I finally find her and she can't remember me!' Red couldn't stop a few tears that fell from his eyes as he helped Leaf stand.

"Hey, why were those guys after you?" Michael asked.

"Oh, they were trying to take this Pichu that I found." Leaf replied as she held up Pichu. A device on Michael's head activated and a scanner appeared in front of his eye.

"I knew it, it's a Shadow Pokémon." Michael replied.

"A what now?" Red asked as he wiped his eyes. Leaf looked at him sadly.

'Did I really know him?' she thought to herself, 'Enough for him to care about me this way?'

"It's is a Pokémon whose heart has been shut in order to release its unrestricted potential." Michael explained, "An organization named Cipher used to make them, until I stopped them. It seems they have some secret Shadow Pokémon, because this one wasn't on the list I recovered that showed all of the ones they made." Leaf tuned Pichu so that it looked at her.

"How can they do something like that to such a cute little Pokémon?" she asked. Michael tried to grab Pichu, but it instantly head butted him, as a purplish aura surrounded it, and jumped back into Leaf's arms.

"Ow...well I guess it'll be your job to purify him." Michael replied.

"How do you know it's a he?" Red asked.

"This PDA tells you everything about a Pokémon." Michael replied. 'Like a pokedex.' Red thought as he turned back to Leaf.

"Leaf, when did you arrive on Orre?" he asked.

"I don't remember arriving." Leaf replied, "I woke up a few days ago and thought I grew up here, but...I was thinking...since you seem to know me so well...you could...help me remember?"

"Of course Leaf." Red replied as his face lit up with relief.

"First thing we should do is find out if Cipher had any secret side projects." Michael commented.

"...Michael?" Red called.

"What?" Michael asked.

"Where is Jovi?" Red asked as he looked around. His question was answered by someone pulling him to the ground and going through his backpack, "Hey, get out of there!" Jovi pulled out the hat Red was carrying and gave it to Leaf.

"Jovi thinks this is yours!" Jovi commented as Red closed his pack and got up.

"This...I remember this!" Leaf replied as she took the hat and put it on, "This really is my hat! How'd you get it?"

"You gave it to me before you left Kanto." Red replied.

"How long have you been carrying that anyways?" Michael asked.

"Two years." Red replied as he looked back at Leaf and smiled, "Two years that were spent looking for the owner."

"Red I...I don't know what to say." Leaf replied, "I don't even remember you and here you are with my hat, telling me you spent two years looking for me and going as far as another region to find me?"

"More than another." Red replied, "I'd go anywhere to find you."

"Red...I...I'm so sorry!" Leaf replied, "Why can't I remember?" Red instinctively hugged her.

"I don't know," he replied, "but I'm going to help you remember."

'Why does this feel...so right?' Leaf thought to herself as she leaned her head on Red's chest.

"Pichu pi!" Pichu cried out as he was being suffocated between Red and Leaf causing them to laugh.

"So you guys want to meet me in Agate Village or come with me to drop off my sister?" Michael asked.

"Agate Village?" Red asked.

"Sorry, I'm getting ahead of myself." Michael replied, "There are two ways to purify a Shadow Pokémon, you can either purify it with the Purify Chamber we have at the Pokémon HQ Lab, or the old fashioned way by taking it to the relic stone when it's ready to open its heart."

"I think the old fashioned way is best." Leaf replied, "But how do we know if it's ready?"

"You can leave that to my PDA." Michael replied, "Just battle with it so that it can get to know you better and open up to you."

"Then we'll meet you there." Red replied. Michael nodded and he led his sister away. Red turned back to Leaf, "What happened to your Ivysuar?"

"I had an Ivysuar?" Leaf asked.

"Don't you have any Pokémon with you?" Red asked.

"No...when I came to, I had a few potions and food, but no Pokémon." Leaf replied, "What about you?"

"I left most of my team at home." Red replied, "I only brought Charizard, Haunter, and-"

"And what?" Leaf asked.

"Your Butterfree!" Red replied with realization as he pulled out a poke ball and sent out Butterfree. Butterfree took a few moments to look around before its eyes landed on Leaf. Almost immediately it flew towards Leaf and hugged her with its stubby arms.

"Butterfree...that's right!" Leaf replied as she returned the hug. Pichu seemed less than happy as it jumped in between Leaf and Butterfree.

"I'm guessing he's not far from being ready, quite the jealous little guy. " Red commented as he called Butterfree back into its poke ball and gave it to Leaf. She smiled, clipped the ball to the waist of her skirt, and placed Pichu in her bag, its head popping out in an adorable fashion. Red took the lead for a moment but quickly stopped.

"What's wrong?" Leaf asked.

"...Michael didn't tell us where Agate Village is." Red laughed as he scratched the back of his head. Leaf couldn't help but laugh as well.

After asking around for directions, Leaf and Red were already on their way to Agate Village when a truck pulled up in front of them and two buff men with armor like uniforms tried to grab them.

"No you don't!" Red shouted as he used one of the guy's chest as a foot hold and drop kicked him in the face, while Leaf dodged the other one, causing him to trip in the process. Pichu jumped out of Leafs bag, "Pichu, Shadow Rush!" Leaf commanded and Pichu became engulfed in a dark purplish aura as he tackled one of the attackers, sending him flying back. Red quickly pulled out a poke ball, "Haunter, give'em a scare!" Red shouted as his Haunter came out, "Hypnosis then Nightmare." Both attackers fell to the ground, twitching at their dream.

"So, these are the Cipher people that Michael talked about?" Leaf asked as she picked up Pichu.

"I guess so." Red replied as he turned to the truck, "Looks like we're getting to Agate Village earlier than we thought.

"You don't even have a permit." Leaf replied.

"So?" Red laughed, "If I'm old enough to battle Pokémon, I should be old enough to drive, no?"

"How old are you anyway?" Leaf asked.

"What?" Red asked, "Oh...right, you don't remember...fifteen."

"Oh...and...h-...how old am I?" Leaf asked as she blushed with embarrassment. Red couldn't help but smile at how cute she looked with that blush.

"You're also fifteen." Red replied.

Once they arrived at Agate Village, they abandoned the truck a ways away since the village was surrounded by a river with only one bridge leading to it. Leaf stared in awe at the beauty of the village, grass covered just about every inch of the ground, water flowed through out the village in small rivers, the doors on the buildings were made of wood, and at the center of the village was a large tree (turned home from what she could see).

"So, do we just wait for Michael here or do we search for the Relic Stone?" Leaf asked.

"I guess we should wait." Red replied, "You want to try battling with Pichu so that he's ready when Michael arrives?"

"Sure, but aren't your Pokémon a little strong?" Leaf asked.

"I'll go easy, we're trying to help Pichu, not torture him." Red Laughed as he sent out Charizard.

Pichu eagerly jumped out of Leaf's bag and jumped up on Charizard's shoulder and began to lightly head butt its neck.

"Let's start." Red suggested and Leaf nodded as they took their places a few feet apart from each other, "Ready?"

"Yep." Leaf replied.

"Charizard use Wing Attack!" Red commanded.

"Dodge Pichu!" Leaf shouted and Pichu successfully dodged Charizard, "Now use Shadow Rush!" Pichu became engulfed in a purplish aura and tackled Charizard, sending him skidding back.

"Whoa, he packs more of a punch than you think!" Red commented, "Alright, Blast Burn!"

"Shadow Rush!" Leaf commanded and Pichu broke into the fiery blast, tackling Charizard down. Pichu and Charizard stayed on the ground, both wiped out, as Red and Leaf neared them. Red recalled Charizard into his poke ball and turned to Leaf, who had picked up Pichu.

"Sorry...I...got carried away." Red apologized.

"I'm not the one you should apologize to!" Leaf replied in an angered tone as she held up Pichu who opened his eyes to find Red in front of him.

"Sorry little guy." Red commented, "Do you forgive me?" Pichu looked at him a bit then jumped out of Leaf's hands, onto Red's head and snuggled its self between Red's head and his cap.

"I think he forgives you if you let him use you as a bed." Leaf laughed. Red got Pichu off his head and gently carried it along as he followed Leaf to a nearby stream. Leaf sat down, took off her shoes and socks, and placed her feet in the cool refreshing water. "This feels nice." she commented as she leaned back on the dirt wall behind her.

"Oh really?" Red asked as placed Pichu down, lifted up Leaf, placed himself between the wall and her, had her lean back to that she leaned on his chest and placed Pichu on her lap, "How about now?"

"B-better..." Leaf replied shyly with a blush, "S-so...you said you traveled more than one region...to find me?"

"Yep." Red replied, "You said you would be gone for a few months (which were hell as I waited to hear from you again), but then you didn't come back six months after you left and I got worried. I searched all over Kanto, but didn't even find a trace. I thought you might've gone to another region for training, so I went over to Johto...but you weren't there. I decided to go all out since it had been ten months since you left, so I headed for the Hoenn region. I met May there-"

"And who is this 'May'?" Leaf asked, surprised at her sudden outburst.

Red chuckled, "She's Brendan's girlfriend. You probably don't remember, but we met Brendan when he went to visit his home region, Johto. Anyways, after turning out empty handed on any trace of you, I headed for the Sinnoh and met up with Dawn there-"

"D-dawn?" Leaf asked.

"Something wrong?" Red asked.

"I...I don't know." Leaf replied, "I get a bad feeling when I hear that name."

"Why? You two were best friends!" Red replied.

"What happened to her?" Leaf asked.

"Well she helped me search for you and ran into her friend, Lucas." Red replied.

Leaf laughed, "Lucas? Was that his real name?"

"Yeah, I know it's funny, but the guy knows how to battle." Red replied, "I think he and Dawn are dating now."

"Huh..."

"What's wrong?" Red asked.

"I don't know, I suddenly felt relieved." Leaf replied, "So, when you didn't find me, you came here?" Leaf asked.

"Yeah." Red replied. Leaf relaxed and closed her eyes, entering a light nap as she rested on Red's arms.

'I feel...so...complete...' Leaf thought, 'but I also feel...awkward. So relaxed and trusting of what could actually be a complete stranger...no. I know him, even if I can't remember, I know Red. I can feel it. I'll remember...no matter what.'

"There you are!" a voice called out. Red and Leaf turned to see Michael walking over to them, "It seems he's ready." Leaf looked down at Pichu who was happily sleeping on her lap.

"So where is the Relic Stone?" Red asked.

"In that cave." Michael responded as he pointed at the cave nearby which the stream came from. Red helped Leaf stand and then picked up Pichu while Leaf grabbed her shoes.

"Hey Red," Michael called out, "Can you give me a hand with this package before we continue?" Red put Pichu on the grass and walked over to help Michael lift a heavy box. Leaf was about to put on her second sock when she began to cough uncontrollably, placing her hands over her mouth to try and muffle it. Once it eased up, she looked at her hands to find them covered in blood.

'Again!?' she thought to herself as she cleaned her hands in the water, 'What's happening to me?'

"Leaf!" Red called out, "Is something wrong?"

"No...my sock just fell in the water." Leaf replied as she discretely wet her sock and twisted it in view so that they could see her trying to dry it. She put on her sock again, ruffing them down a bit so that they weren't smooth and couldn't reach her knees, then put on her shoes, picked up Pichu and placed him in her bag, then caught up to Red and Michael.

"What's in this box?" Red asked as they carried it up the hill.

"Poke food." Michael replied, "Eagun's Pikachu eats a lot, we'll just drop this off and go purify Pichu."

"You help around a lot don't you?" Leaf asked.

"Yeah." Michael laughed. "We're here." He exclaimed as they stopped in front of the giant tree home, "I'll let Eagun know that the foods here, you guys go purify Pichu." Leaf began to cough again.

"Leaf, you ok!?" Red asked.

"I'm fine." Leaf replied as he turned away, but she couldn't hide the large amount of blood that spilled onto the floor as her cough worsened.

"Leaf!" Red called out as he gently turned her so that she looked at him. Red was shocked as he saw the blood in her hands and a bit left on her mouth, trailing down her chin, "Leaf, what happened!?"

"I'm ok, really!" Leaf replied as she tried to get away, but Red didn't let go, "Red, let-"

"No." Red replied, "What's going on? Why are you bleeding? Who hurt you?"

"I don't know!" Leaf cried as she leaned on Red's chest, "Its been happening since I woke up here! I can't stop it! I'm scared Red!" Red hugged her tight as she cried into his chest, trying to calm her as he thought of what he could do. Before Red could come up with a solution though, something big caught everyone's attention. Dark clouds filled the sky, shutting out all light from above. Lightning flew left and right, setting nearby patches of grass on fire. Soon a dark figure emerged from the clouds, covered in a purplish aura.

"Lugia!" Michael shouted as he threw a poke ball, unleashing Lugia into the sky, "Use Aeroblast!" Lugia brought its massive wings in front of his face and swung them out as a large bullet like blast of wind emerged and headed for the attacking figure, hitting it dead on. The figure didn't even flinch as it reared back its head and fired a shadowy beam at Lugia, knocking it out in one hit. Michael returned Lugia to its poke ball.

"What is that?" Michael asked Red who had watched in awe and realization.

"A-a...shiny Rayquaza?" Red asked as Rayquaza let out a power demonstrating roar. A human figure appeared on Rayquaza's head.

"People of Agate Village!" the figure shouted with its arms outstretched, "Behold Cipher's secret project, the SHADOW RAYQUAZA!" Rayquaza let out another roar. "Our test beacon has chosen your village as the first to die a slow death! Rayquaza, Shadow Death!" Rayquaza roared into the sky and fired a purple smokescreen.

"RED, DON'T BREATHE!" Leaf shouted, but the smokescreen quickly covered the village and lingered, making it impossible to avoid. Red noticed that the smokescreen didn't smell, taste, or even interfere with breathing.

"You have one week to live!" the voice shouted, "And a message to the beacon, your time has been reset. If you wish to reset it again and live on, you must designate more targets!" Rayquaza roared one last time before it disappeared and the sky cleared.

"That was...Ardos!" Michael exclaimed, "But what did he mean with that?"

"I'm not sure, but-" Red didn't finish, due to a coughing fit that suddenly took over. He finally suppressed it and looked at his hand, only to find a small amount of blood on it. Others began to cough, including Michael and Leaf. Leaf looked up at Red with fear as she showed him that she didn't cough up as much blood as before.

"Leaf is the beacon?" Michael asked with surprise.


End file.
